@subsection Extracting the meta-QTL

Now, suppose we want to get the 7 meta-QTL of the chromosome 1 separetly on the consensus map. To do so, we can use the command @code{QTLModel} as follows:

@cartouche
@example
$java org.metaqtl.main.QTLModel -m meta-map/consensus_map.xml \
                                -r meta-qtl/meta-analysis_1_res.txt \
				-b meta-qtl/meta-analysis_1_best.txt \
				-o meta-post/metamap.xml
@end example
@end cartouche
@noindent

Then, if we use @code{MapView} to display the map @file{metamap.xml} we obtain something like that:

@float
@image{fig21,16cm,4cm,,}
@end float

@subsection Projection of the meta-QTL

Finally, it could be useful to project the meta-QTL onto a reference map which provides candidate genes in order to study the congruency between these candidate genes and the meta-QTL.

Then, suppose we want to project the meta-QTL onto the reference map @code{genetic_2005} which we have previously used. So, we can use the program @code{QTLProj} as follows:

@cartouche
@example
$java org.metaqtl.main.QTLProj -m ref-map/genetic_2005.xml \
                               -q meta-post/metamap.xml \
			       -o meta-post/genetic_2005 \
			       --verbose
@end example
@end cartouche
@noindent

Then, if we use @code{MMapView} to display the result of the projection we obtain something like that:

@float
@image{fig22,10cm,15cm,,}
@end float

